> We have high res monitors with incredible graphical capabilities but we still mostly just represent code as flat text files

I think the key issue here is that flat text files remain an universal standard, easily handled with commodity tools and editors, often bundled with the OS itself.

Once in a while someone wants to revolutionize code representation (like Light Table, which you mentioned). "What if we represented code as a... flowchart, a graph of nodes, a city, a pie chart, a mind map, $YOUR_NOVEL_IDEA_HERE? Wouldn't that be great and take advantage of current hardware to the fullest?"

It turns out it's really hard to beat good old flat text at convenience and interoperability with standard tools.